Cloud Analysis enables cell type annotation for standard Cell Ranger and Cell Ranger ARC outputs to generate accurate cell type labels. The cell annotation models are currently under beta development.

This example shows how to run the annotate pipeline and outlines the expected output files using a publicly available dataset.

• A successfully completed run of standard Cell Ranger (count, multi, aggr) or Cell Ranger ARC (count, aggr) pipelines on Cloud Analysis, with a dataset that includes a Gene Expression library. These pipelines must be run in Cloud Analysis, as you cannot begin by uploading Cell Ranger or Cell Ranger ARC outputs to the 10x Cloud.
• A .cloupe file will only be generated if secondary analysis is enabled during the initial run.
• The sample must be human (or human-derived) or mouse (or mouse-derived).
• The analysis supports datasets ranging from 100 to 800,000 cells.
• The availability of automated cell annotation is subject to restrictions based on U.S. or local laws and regulations. See regional restrictions for the list of impacted regions.

1. Go to the Analysis tab in the web interface and select the analysis you wish to annotate.
2. Click the "Run Cell Type Annotation" button to start setting up.

This will take you to the annotation setup page:

• Provide a descriptive name for your analysis to help you easily identify it later.
• If desired, you can rename the "Cell Type Category" that appears in Loupe Browser.
• There are no tunable parameters in the cell annotation algorithm at this time. As additional models are released, you will be able to select your preferred model, but no further customization options will be available.

3. Click "Run Annotation" to begin the process. You will receive an email notification once the analysis is complete.

The following output files are provided from the annotation pipeline. Detailed descriptions of the output file contents are available on the Cell Ranger support website.